Object transformations not applying when running Blender in batch mode
From the API documentation:

By default handlers are freed when loading new files, in some cases you may wan’t the handler stay running across multiple files (when the handler is part of an addon for example).
For this the bpy.app.handlers.persistent decorator needs to be used.

import bpy
from bpy.app.handlers import persistent

@persistent
def load_handler(dummy):
    print(&quot;Load Handler:&quot;, bpy.data.filepath)

bpy.app.handlers.load_post.append(load_handler)